Russian Academy of Sciences Siberian Branch Institute of Cytology and Genetics Laboratory of Theoretical Genetics Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure

Motivation: Eukaryotic chromosomes are organized in loops. Bases of chromatin loops are attached to chromosome axes; in meiosis, these are protein axes forming the synaptonemal complex (SC). Earlier, SC attachment regions (SCAR DNA) were isolated and characterized in rat and hamster. Their sequences were shown to form a specific family (Karpova et al., 1995). Hence the problem was to develop a method of in silico searching for specific SCAR DNA-like meiotic sequences (mei-DNA) in genomes of other organisms. Detection of mei-DNA would pose the following questions: (1) whether mei-DNA plays a part in the formation and/or topography of lateral chromatin loops and (2) how is mei-DNA related to sites of meiotic recombination. Results: A method was developed to in silico search the mammalian genomes for specific repetitive sequences (RS) similar to SCAR DNA. The chromosome distribution of these (mei-DNA) sequences was characterized. The frequency of mei-DNA sites in the Y chromosome is almost thrice lower than in autosomes in human. Autosomal mei-DNA sites are mostly 10 or 50–60 kb apart, suggesting clustering. The meiotic recombination frequency is minimal in sites of predominant mei-DNA location. The results agree with the fact that most of the Y chromosome is not involved in the SC formation or meiotic recombination and with the model implying that mei-DNA sequences contact the SC central element and lie at the bases of lateral chromatin loops, while recombination initiation sites are more often located in central regions of the loops.